Eutrophication caused by excess nutrient loads is the main problem for Estonian surface waters. Even after the drastic decrease in the application of mineral fertilizers at the beginning of the 1990s, the concentrations of nitrogen and phosphorus in many rivers remained at undesirable and unexpectedly high levels. The investigation showed that drained peat soils are an important source of nitrogen export to the surface waters. Runoff of nitrogen from drained peat soils is, on average, 1.5-fold higher than from agricultural lands in Estonia.